[Bio] / FigKernelScripts / promote_orfs_to_pegs.pl Repository:
ViewVC logotype

Annotation of /FigKernelScripts/promote_orfs_to_pegs.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.4 - (view) (download) (as text)

1 : overbeek 1.1 # -*- perl -*-
2 :     #
3 :     # Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :     # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 :     #
8 :     # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 :     # Public License.
11 :     #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 :     #
18 :    
19 :     use FIG;
20 :     my $fig = new FIG;
21 :    
22 :     use NewGenome;
23 :     use ToCall;
24 :    
25 :     my $usage = "usage: promote_orfs_to_pegs To_Call_Dir";
26 :    
27 :     if (@ARGV && ($ARGV[0] =~ m/-h(elp)?/)) {
28 :     print STDERR "\n $usage\n\n";
29 :     exit (0);
30 :     }
31 :    
32 :     my ($to_call_dir);
33 :    
34 :     (
35 :     ($to_call_dir = shift @ARGV)
36 :     )
37 : overbeek 1.2 || die "\n $usage\n\n";
38 : overbeek 1.1
39 : overbeek 1.3 $to_call_dir =~ s/\/$//o;
40 :    
41 : overbeek 1.1 my $to_call;
42 :     $to_call = new NewGenome($to_call_dir,"all");
43 :     $to_call->promote_remaining_orfs;
44 :     $to_call->export_features;
45 : overbeek 1.2
46 : overbeek 1.4 if (! -s "$to_call_dir/Features/orf/tbl") {
47 : overbeek 1.2 &FIG::run("rm -fR $to_call_dir/Features/orf");
48 :     }
49 :     else {
50 :     die "Something is wrong --- $to_call_dir/Features/orf/tbl is non-empty";
51 :     }

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3